Expanded Carrier Screening with NGS

CarrierSeq NGS solutions for expanded carrier screening

In today’s multiethnic society, some genetic disorders previously thought to be confined to specific ethnic groups are increasingly being found in broader populations. NGS enables rapid carrier screening research across the broadest range of disorders, crossing ancestries and geographic regions, with a scalable, cost-effective solution.

 

Implement pan-ethnic, expanded carrier screening (ECS) research in your lab with a comprehensive solution from Thermo Fisher Scientific, including Ion Torrent CarrierSeq ECS kits and Carrier Reporter Software for the Ion GeneStudio S5 System. This next-generation sequencing (NGS)-based end-to-end solution includes rigorously designed targeted content for genetic analysis, optimized reagents for peak performance, and intuitive data analysis software tools for streamlined implementation, even in labs new to NGS.

Why labs choose targeted NGS for expanded carrier screening research

 

Focused

Only genes or regions known to be linked to inherited disorders are sequenced to help ensure precision and relevance in genetic analysis. 

 

Sensitive

Identifies rare or novel variants with higher read depth to enable greater accuracy than other NGS methods

 

Efficient

Produces relatively small datasets, reducing time and resources for sequencing and data analysis.

Key benefits of expanded carrier screening with CarrierSeq ECS Kits

Screen for a broad range of inherited disorders

 

A 420-gene panel targeting the full coding region of all genes enables the analysis of >36,000 non-benign ClinVar variants for single-nucleotide variants (SNVs), insertions and deletions (indels), and copy number variants (CNVs) by NGS

Consolidate stand-alone assays to improve lab efficiency

 

NGS enables simultaneous screening of hundreds of genes in one experiment, providing information on a broader range of targets with a faster turn-around time than traditional techniques such as PCR or Sanger sequencing

An end-to-end solution from a single vendor

 

CarrierSeq ECS kits include reagents for library preparation, template preparation, and sequencing, plus software for data analysis and reporting. Leveraging Ion AmpliSeq technology, these optimized assay kits streamline implementation and help ensure reliable and consistent results

Easily implement NGS-based carrier screening with ACMG Tier 3 genes in your research lab

CarrierSeq ECS kits are now available with a supplemental panel for coverage of 447 genes, including 111 American College of Medical Genetics and Genomics (ACMG) Tier 3 genes.

Hear from CarrierSeq ECS users

Bruno Coprerski
Head of IVF, Igenomix, Brazil

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    Expanded carrier screening clinical research with Ion Torrent CarrierSeq ECS

    Rigorously designed content and consolidated assays

    CNV detection is an essential part of genetic analysis for inherited disorders. But genetic variants for a number of the most severe yet prevalent disorders can be challenging to detect by NGS assays. Our algorithms have been optimized to overcome the difficulties in variant calling from pseudogenes, paralogues, or related homology issues. Confirmation of findings via an orthogonal testing method is recommended.

    420-gene-screening-panel-large Figure 1: Content for increased detection rates.

    Streamlined implementation and workflow

    CarrierSeq ECS Kit reagents are optimized to work together out of the box (Figure 2). Using the Ion Chef and Ion GeneStudio S5 systems for template preparation and sequencing, plus a suite of software programs for data analysis, CarrierSeq ECS Kits offer a seamless workflow for carrier screening research.

    Streamlined workflow for 32 samples Figure 2. Streamlined workflow for 32 samples—fast turnaround from genomic DNA to variant calls.
    Ion Torrent CarrierSeq ECS Panel based on Ion AmpliSeq technology. Automated with pre-packaged, ready-to-use reagent cartridges. Pre-packaged reagent cartridges for fast, easy set-up. Choice of two Ion Chip kits, for scalable throughput needs. Customizable analysis and reporting options, to quickly translate data into results.
    Total time: 8 hours (32 samples)
    Hands-on time: 120 min    		 Total time: 14.5 hours
    Hands-on time: 15 min    		 Total time: 6 hours
    Sequencing per chip: 2.75 hours
    Hands-on time:15 min    		 Total time: 4–16.5 hours (depending on instrument compute)
    Total time: 2 hours (Ion Reporter)
    Hands-on time: 5 min

    For library preparation, CarrierSeq ECS kits use the globally recognized, superior Ion AmpliSeq technology, a fast and simple amplicon-based enrichment method for targeted NGS. This proprietary, proven technology combines thousands of primer pairs into a single PCR reaction for robust and consistent library preparation.

     

    CarrierSeq ECS kits are available in 4 or 16 samples per chip (8 or 32 samples per run). Variable throughput on a single system streamlines the path to increasing carrier screening research or transitioning from outsourcing to an in-house platform.

     

    Straightforward and powerful data analysis

    Carrier Reporter Software automatically classifies carrier variants based on pathogenicity according to ClinVar, proprietary databases, and the American College of Medical Genetics and Genomics (ACMG) predicted pathogenicity guidelines. It also enables users to customize variant classifications based on user-defined guidance. This intuitive software interface presents: sequencing QC information, carrier results with notification icons to streamline the review process, and reference web links to view supporting variant calling evidence. Additionally, Carrier Reporter customization enables the analysis and reporting of only the variants and genes of interest.

    Carrier Reporter Software sample case report

    Carrier Reporter Software key features and usability video

    Torrent Suite Software

    Plan, monitor, and track your runs within a browser, while reviewing the quality and accuracy of your sequencing run.

    Ion Reporter Software

    Identify variants such as SNVs, indels, and CNVs with preconfigured and customizable workflows, providing flexibility for users of any experience level.

    Carrier Reporter Software

    Classify variants according to pathogenicity based on ACMG and ClinVar guidelines. Customize analysis and reporting at variant and gene levels.

    Figure 3. Straightforward bioinformatics workflow.

    Expanded carrier screening kit and panel ordering information

    For Research Use Only. Not for use in diagnostic procedures.